/**
 * @file src/Settings.cpp
 *
 * @date 10-may-2013
 *
 * @author Youri Hoogstrate
 * @author Lisa Yu
 *
 * @section LICENSE
 * yh-kt-fold can predict RNA 2D structures including K-turns.
 * Copyright (C) 2012-2013 Youri Hoogstrate
 *
 * This file is part of yh-kt-fold.
 *
 * yh-kt-fold is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 *
 * yh-kt-fold is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program. If not, see <http://www.gnu.org/licenses/>.
 */



#include "main.h"



/**
 * @brief Takes care of the input, arguments and stores the settings.
 *
 * @section DESCRIPTION
 * Handling the arguments, settings and input.
 *
 * @date 10-may-2013
 */
class Settings
{
	private:
		// Pass through parameters: should be passed through to Zuker class.
		int SETTING_MIN_HAIRPINLEN;
		
		// Global parameters: defines which functions of Zuker should be called.
		bool SETTING_ENABLE_MOTIF_FUNCTIONALITY;
		bool SETTING_USE_CLASSICAL_TRACEBACK;
		
		/** @todo: Use pointers instead. */
		char SETTING_SEQUENCE[3000];
		char SETTING_PROGRAM_NAME[256];
		
		// Requested parameters
		int argc;
		char **argv;
		
	public:
		Settings(int arg_argc, char *arg_argv[]);
		
		// Get functions
		bool get_enableMotifFunctionality();
		bool get_useClassicalTraceback();
		int get_minHairpinlen();
		
		// Copy functions
		void copy_sequence(char *sequence_string);
		
		// Parse functions
		void parseParameters();
		void parseSequenceFromStream(FILE *stream);
		
		// Print functions
		void printUsage();
		void printVersion();
};
